Denis Roy
Université Laval, Food Sciences, Faculty Member
- Denis Roy is Full Professor with the Department of Food Sciences of the Université Laval (Quebec, Canada). He is an ... moreDenis Roy is Full Professor with the Department of Food Sciences of the Université Laval (Quebec, Canada). He is an expert in the field of probiotics and prebiotics and former Tier I holder of the Canada Research Chair in Lactic Culture Biotechnology for Dairy and Probiotic Industries (2003-2017). His research interests focuses on functional food- and colon-related microbial cultures, with attention to their functioning, properties, and potential health benefits. Molecular approaches such as metagenomics and metatranscriptomics are applied to define the diversity and to measure the gene expression of microbial communities found in the intestinal tract of animal and human or in food systems.edit
Extracellular tannase Lactiplantibacillus plantarum-producing strains (TanA+) release bioactive metabolites from dietary tannins. However, there is a paucity of knowledge of TanA+ strains and their hydrolyzing capacities. This study aimed... more
Extracellular tannase Lactiplantibacillus plantarum-producing strains (TanA+) release bioactive metabolites from dietary tannins. However, there is a paucity of knowledge of TanA+ strains and their hydrolyzing capacities. This study aimed to shed light on the metabolic and genomic features of TanA+ L. plantarum strains and to develop a screening technique. The established spectrophotometric was validated by UPLC-UV-QToF. Eight of 115 screened strains harbored the tanA gene, and six presented TanA activity (PROBI S126, PROBI S204, RKG 1-473, RKG 1-500, RKG 2-219, and RKG 2-690). When cultured with tannic acid (a gallotannin), TanA+ strains released 3.2−11 times more gallic acid than a lacking strain (WCFS1) (p < 0.05). TanA+ strains with gallate decarboxylase (n = 5) transformed this latter metabolite, producing 2.2–4.8 times more pyrogallol than the TanA lacking strain (p < 0.05). However, TanA+ strains could not transform punicalagin (an ellagitannin). Genomic analysis reveal...
Consumption of red raspberries has been reported to exert acute beneficial effects on postprandial glycemia, insulinemia, triglyceridemia, and cytokine levels in metabolically disturbed subjects. In a two-arm parallel-group, randomized,... more
Consumption of red raspberries has been reported to exert acute beneficial effects on postprandial glycemia, insulinemia, triglyceridemia, and cytokine levels in metabolically disturbed subjects. In a two-arm parallel-group, randomized, controlled trial, 59 subjects with overweight or abdominal obesity and with slight hyperinsulinemia or hypertriglyceridemia were randomized to consume 280 g/day of frozen raspberries or to maintain their usual diet for 8 weeks. Primary analyses measured metabolic differences between the groups. Secondary analyses performed with omics tools in the intervention group assessed blood gene expression and plasma metabolomic changes following the raspberry supplementation. The intervention did not significantly affect plasma insulin, glucose, inflammatory marker concentrations, nor blood pressure. Following the supplementation, 43 genes were differentially expressed, and several functional pathways were enriched, a major portion of which were involved in th...
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The temporal instability of raw milk microbiota drastically affects the reliability of microbiome studies. However, little is known about the microbial integrity in preserved samples. Raw cow milk samples were preserved with azidiol or... more
The temporal instability of raw milk microbiota drastically affects the reliability of microbiome studies. However, little is known about the microbial integrity in preserved samples. Raw cow milk samples were preserved with azidiol or bronopol and stored at 4 °C, or with dimethyl sulfoxide (DMSO) or a mixture of azidiol and DMSO and stored at −20 °C for up to 30 days. Aliquots of 5-, 10-, and 30-day post-storage were treated with propidium monoazide (PMA), then analyzed by sequencing the 16S rRNA gene V3-V4 and V6-V8 regions. The V6-V8 gave a higher richness and lower diversity than the V3-V4 region. After 5-day storage at 4 °C, the microbiota of unpreserved samples was characterized by a drastic decrease in diversity, and a significant shift in community structure. The treatment with azidiol and DMSO conferred the best community stabilization in preserved raw milk. Interestingly, the azidiol treatment performed as well for up to 10 days, thus appearing as a suitable alternative. H...
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Lactobacillus strains are known to produce exopolysaccharides (EPS) with recognized health benefits (i.e. prebiotic and immunomodulation) but production is limited by low yields. Co-culture has been shown to improve metabolite... more
Lactobacillus strains are known to produce exopolysaccharides (EPS) with recognized health benefits (i.e. prebiotic and immunomodulation) but production is limited by low yields. Co-culture has been shown to improve metabolite productivity, particularly bacteriocins and EPS. Although lactic acid bacteria (LAB) and yeasts are found in several fermented products, the molecular mechanisms linked to the microbial interactions and their influences on EPS biosynthesis are unclear. The aim of the present study was to investigate the effect of co-culture on EPS production by three Lactobacillus rhamnosus strains (ATCC 9595, R0011, and RW-9595M) in association with Saccharomyces cerevisiae. Fermentation, in both mono and co-culture, was carried out and the expression of key LAB genes was monitored. After 48 h, results revealed that EPS production was enhanced by 39%, 49%, and 42% in co-culture for R0011, ATCC 9595, and RW-9595M, respectively. Each strain showed distinctive gene expression pr...
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Inflammatory bowel diseases (IBDs) are multifaceted and relapsing immune disorders, which necessitate long-term dependence on powerful drugs. As the use of natural product-based therapies has emerged as a promising intervention, the... more
Inflammatory bowel diseases (IBDs) are multifaceted and relapsing immune disorders, which necessitate long-term dependence on powerful drugs. As the use of natural product-based therapies has emerged as a promising intervention, the present study aimed to further characterize dried apple peel powder (DAPP) mechanisms of action and evaluate the preventive and curative effects of DAPP on mitochondrial functions in a murine model. Induction of intestinal inflammation in mice is performed by oral administration of the dextran sodium sulfate (DSS) at 2.5% for 10 days. Doses of DAPP (200 or 400 mg/kg/day) were administered by gavage for 10 days pre- and 1 day after colitis induction simultaneously with DSS treatment for a period of 10 days. The preventive (200 mg/kg/day) and therapeutic (400 mg/kg/day) doses of DAPP limited DSS-induced histological lesions, improved macroscopic parameters and attenuated clinical signs. DAPP at the same conditions reduced massive infiltration of inflammato...
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There is growing evidence that fruit polyphenols exert beneficial effects on the metabolic syndrome, but the underlying mechanisms remain poorly understood. In the present study, we aimed to analyse the effects of polyphenolic extracts... more
There is growing evidence that fruit polyphenols exert beneficial effects on the metabolic syndrome, but the underlying mechanisms remain poorly understood. In the present study, we aimed to analyse the effects of polyphenolic extracts from five types of Arctic berries in a model of diet-induced obesity. Male C57BL/6 J mice were fed a high-fat/high-sucrose (HFHS) diet and orally treated with extracts of bog blueberry (BBE), cloudberry (CLE), crowberry (CRE), alpine bearberry (ABE), lingonberry (LGE) or vehicle (HFHS) for 8 weeks. An additional group of standard-chow-fed, vehicle-treated mice was included as a reference control for diet-induced obesity. OGTTs and insulin tolerance tests were conducted, and both plasma insulin and C-peptide were assessed throughout the OGTT. Quantitative PCR, western blot analysis and ELISAs were used to assess enterohepatic immunometabolic features. Faecal DNA was extracted and 16S rRNA gene-based analysis was used to profile the gut microbiota. Trea...
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Previous studies have reported that polyphenol-rich extracts from various sources can prevent obesity and associated gastro-hepatic and metabolic disorders in diet-induced obese (DIO) mice. However, whether such extracts can reverse... more
Previous studies have reported that polyphenol-rich extracts from various sources can prevent obesity and associated gastro-hepatic and metabolic disorders in diet-induced obese (DIO) mice. However, whether such extracts can reverse obesity-linked metabolic alterations remains unknown. In the present study, we aimed to investigate the potential of a polyphenol-rich extract from cranberry (CE) to reverse obesity and associated metabolic disorders in DIO-mice. Mice were pre-fed either a Chow or a High Fat-High Sucrose (HFHS) diet for 13 weeks to induce obesity and then treated either with CE (200 mg/kg, Chow + CE, HFHS + CE) or vehicle (Chow, HFHS) for 8 additional weeks. CE did not reverse weight gain or fat mass accretion in Chow- or HFHS-fed mice. However, HFHS + CE fully reversed hepatic steatosis and this was linked to upregulation of genes involved in lipid catabolism (e.g., PPARα) and downregulation of several pro-inflammatory genes (eg, COX2, TNFα) in the liver. These findings...
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Diets rich in fruits and vegetables may reduce oxidative stress and inflammation via several mechanisms. These beneficial effects may be due to their high polyphenol content. The aims of the present study are to evaluate the preventive... more
Diets rich in fruits and vegetables may reduce oxidative stress and inflammation via several mechanisms. These beneficial effects may be due to their high polyphenol content. The aims of the present study are to evaluate the preventive and therapeutic aspects of polyphenols in dried apple peel extract (DAPP) on intestinal inflammation while elucidating the underlying mechanisms and clinical benefits. Induction of intestinal inflammation in mice was performed by oral administration of the inflammatory agent DSS at 2.5% for 10 days. Physiological and supraphysiological doses of DAPP (200 and 400 mg/kg/day, respectively) were administered by gavage for 10 days pre- and post-DSS treatment. DSS-mediated inflammation caused weight loss, shortening of the colon, dystrophic detachment of the epithelium, and infiltration of mono- and polymorphonuclear cells in the colon. DSS induced an increase in lipid peroxidation, a down-regulation of antioxidants, an augmented MPO and COX2, an elevated P...
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Arabinoxylan oligosaccharides (AXOS) are a promising class of prebiotics that have the potential to stimulate the growth of bifidobacteria and the production of butyrate in the human colon, known as the bifidogenic and butyrogenic... more
Arabinoxylan oligosaccharides (AXOS) are a promising class of prebiotics that have the potential to stimulate the growth of bifidobacteria and the production of butyrate in the human colon, known as the bifidogenic and butyrogenic effects, respectively. Although these dual effects of AXOS are considered beneficial for human health, their underlying mechanisms are still far from being understood. Therefore, this study investigated the metabolic interactions betweenBifidobacterium longumsubsp.longumNCC2705 (B. longumNCC2705), an acetate producer and arabinose substituent degrader of AXOS, andEubacterium rectaleATCC 33656, an acetate-converting butyrate producer. Both strains belong to prevalent species of the human colon microbiota. The strains were grown on AXOS during mono- and coculture fermentations, and their growth, AXOS consumption, metabolite production, and expression of key genes were monitored. The results showed that the growth of both strains and gene expression in both s...
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ABSTRACT Cranberry consumption has been demonstrated to improve features of the metabolic syndrome, therefore providing an alternative strategy to prevent obesity and type-2 diabetes. Moreover, gut dysbiosis is now considered as a key... more
ABSTRACT Cranberry consumption has been demonstrated to improve features of the metabolic syndrome, therefore providing an alternative strategy to prevent obesity and type-2 diabetes. Moreover, gut dysbiosis is now considered as a key factor in metabolic disorders. In order to understand the involvement of phenolic compounds in the health-improving effects of cranberry, this study aimed to investigate their bioavailability after oral administration of a cranberry extract (CE) to high-fat high-sucrose (HFHS) fed mice, and to explore a possible modulation of gut microbiota composition following a co-supplementation with spores of Bacillus subtilis CU1 probiotic (CE/P). Phenolic metabolites were extracted and characterized from plasma using μSPE-UHPLC-MS/MS, and a metagenomic analysis was performed on feces to assess gut bacterial composition. 22 circulating metabolites were identified, mainly microbial degradation products of native cranberry phenolic compounds. Plasma concentration of 3 microbial metabolites was significantly increased with the CE/P co-treatment: p-coumaric acid, m-coumaric acid and p-hydroxybenzoic acid (+ 53%, + 103% and + 70% respectively). Associated to this modulation, we reported significant differences in the proportion of Barnesiella and Oscillibacter genera in CE/P treated mice in comparison with control animals. This study thus highlights the impact of an altered gut microbiota on phenolic compounds degradation and bioavailability in mice.
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The luciferin-luciferase bioluminescence method was used to estimate the number of bacteria retained in neutral and amphiphilic gels and those in the eluate to determine the hydrophobic surface properties of bacteria by using hydrophobic... more
The luciferin-luciferase bioluminescence method was used to estimate the number of bacteria retained in neutral and amphiphilic gels and those in the eluate to determine the hydrophobic surface properties of bacteria by using hydrophobic interaction chromatography. Good correlations were found between viable counts and ATP content for Escherichia coli, Pseudomonas fragi, and Listeria monocytogenes. ATP determination was more rapid than viable counts for characterizing the relative hydrophobicity of L. monocytogenes. Quantitative estimations of adsorption of L. monocytogenes on octyl-Sepharose indicate that this microorganism is hydrophilic.
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The susceptibility of planktonic and biofilm cells of Pseudomonas marginalis toward four commonly used biocides at different temperatures (15 and 30 degrees C) and biofilm growth times (24 and 48 h) was assessed. Using the MBEC biofilm... more
The susceptibility of planktonic and biofilm cells of Pseudomonas marginalis toward four commonly used biocides at different temperatures (15 and 30 degrees C) and biofilm growth times (24 and 48 h) was assessed. Using the MBEC biofilm device, biofilm production in maple sap was shown to be highly reproducible for each set of conditions tested. Biofilm formation was influenced by growth temperature and time. A temperature of 15 degrees C and incubation time of 24 h yielded fewer CFU per peg and showed fewer adhered cells and typical biofilm structures, based on scanning electron microscopy observations as compared with other conditions. Minimal biofilm eradication concentration values for P. marginalis were significantly greater (P. < 0.001) than were MBCs for planktonic cells and for every biocide tested, with the exception of minimal biofilm eradication concentration values for peracetic acid at 15 degrees C and 24 h. Sodium hypochlorite and peracetic acid sanitizers were able ...
Research Interests: Biofilms, Scanning Electron Microscopy, Scanning Transmission Electron Microscopy, Multidisciplinary, Food Microbiology, and 12 morePseudomonas, Temperature, Hygiene, Anti-Bacterial Agents, Sodium Hypochlorite, Acer, Time Factors, Microbial Sensitivity Tests, Food Contamination, Food Handling & Hygiene, Peracetic Acid, and food handling
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In this study, ribosomal intergenic spacer analysis (RISA) was used to monitor changes of intestinal microbiota of piglets treated at birth with or without Pediococcus acidilactici (PA) and/or Saccharomyces cerevisiae ssp. boulardii (SCB)... more
In this study, ribosomal intergenic spacer analysis (RISA) was used to monitor changes of intestinal microbiota of piglets treated at birth with or without Pediococcus acidilactici (PA) and/or Saccharomyces cerevisiae ssp. boulardii (SCB) and weaned piglets fed with control diet supplemented with PA and/or SCB or antibiotic. During lactation, probiotics were given orally to piglets three times a week. At weaning (day 21), probiotics and the antibiotic, tiamulin, were added to the diet. Fifteen piglets per treatment were slaughtered at day 18 and day 24. The tracking of each probiotic from colonic samples was done using PCR primers specific for PA targeting the 16S rRNA gene or a specific culture medium for enumeration of SCB. The results showed the presence of probiotics in colonic samples of piglets supplemented with probiotics. Dendograms (UPGMA and Ward’s method), and non-metric multidimensional scaling analysis showed that the variability of RISA profiles in colonic microflora b...
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The intestinal microbiota is the largest source of microbial stimulation that exerts both harmful and beneficial effects on human health. The interaction between probiotic and enterocytes is the initiating event in immunomodulation and... more
The intestinal microbiota is the largest source of microbial stimulation that exerts both harmful and beneficial effects on human health. The interaction between probiotic and enterocytes is the initiating event in immunomodulation and merits particular attention. The effects of probiotic is strain dependent and for each new probiotic strain, profiles of cytokines secreted by lymphocytes, enterocytes or dendritic cells that come in contact with the strain should be systematically established. To evaluate the effects of probiotics on the immune system, models that mimic the mucosa, and thus the physiological reality, should be preferred whenever it is possible. Then, the in vitro observed effects should be backed up by properly conducted randomized double bind clinical studies. More detailed studies are needed to determine the precise action mode of probiotics on both mucosal and systemic immunity.
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Forty Bacillus isolates obtained from maari (used as condiment in Burkina Faso) including 17 B. subtilis, 4 B. circulans, 7 B. pumilus and 6 B. licheniformis were investigated for use as starter cultures in maari production. The isolates... more
Forty Bacillus isolates obtained from maari (used as condiment in Burkina Faso) including 17 B. subtilis, 4 B. circulans, 7 B. pumilus and 6 B. licheniformis were investigated for use as starter cultures in maari production. The isolates were screened by PCR for the sfp gene responsible for the production of the lipopeptide biosurfactant, surfactin. The sfp gene was detected in all of the seventeen B. subtilis isolates, in 2 out of 7 B. pumilus, in 4 out of 6 B. licheniformis whereas no B. circulans was positive for the sfp gene by PCR screening. Furthermore, all the 40 Bacillus spp. were screened for biosurfactant production and inhibitory activity against Aspergillus flavus, A. niger, A. versicolor and Rhizopus oryzae. Results demonstrated a relationship between the presence of the sfp gene and the antifungal activity and biosurfactant production of Bacillus isolates. In addition, molecular typing of the 17 B. subtilis isolates by Multilocus Sequence Typing (MLST) resulted in 15 Sequence Types, one of them included three strains. Randomly Amplified Polymorphic DNA-PCR (RAPD-PCR), used for B. licheniformis, B. megaterium, B. circulans and B. pumilus revealed that the inhibitory activity and biosurfactant production were strain-dependent. Finally, the detection of chitinase (chi) and β-glucanase (glu) biosynthesis genes was found to be associated with the antifungal activity for 16 B. subtilis isolates. The present work provides a greater understanding of the antifungal activity and biosurfactant production ability within the Bacillus spp. isolated from maari and contributes to the selection of Bacillus isolates to be used as starter cultures for controlled production of maari.
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Research Interests: Genetics, Microbiology, Industrial Biotechnology, Sequence Analysis, Food Microbiology, and 13 moreGenetic Diversity, Cluster Analysis, Industrial Application, Genetic Polymorphism, Food Sciences, Genetic variation, Amino Acid Profile, Species Specificity, Starter Culture, Genetic Markers, Lactococcus lactis, Comparative Genomic Hybridization, and Multilocus sequence typing
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Research Interests: Microbiology, Carbon Dioxide, Population Dynamics, Filtration, Industrial Biotechnology, and 20 moreFood Microbiology, Quantitative PCR, Food Preservation, Population structure, Gene Cloning, Humans, SHELF LIFE, Animals, Bacteria, Microfiltration, Population Growth, Milk, Time Factors, Food Contamination, Food Sciences, Raw Milk, Food Handling & Hygiene, Cold Storage, Ribosomal DNA, and Microbial community
Research Interests: Multidisciplinary, Antibiotic Resistance, Phylogeny, Lactic Acid Bacteria, Gram Positive, and 13 moreApplied Environmental Microbiology, Primer design, Polymerase Chain Reaction, Phylogenetic analysis, Lactobacillus Casei, Gram-negative bacteria, Specific Activity, Degeneration, Glycosyltransferases, Amino Acid Profile, Amino Acid Sequence, Bacterial Infection, and Oligonucleotides
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Thousands of genes in a genomewide data set are tested against some null hypothesis, for detecting differentially expressed genes in microarray experiments. The expected proportion of false positive genes in a set of genes, called the... more
Thousands of genes in a genomewide data set are tested against some null hypothesis, for detecting differentially expressed genes in microarray experiments. The expected proportion of false positive genes in a set of genes, called the False Discovery Rate (FDR), has been proposed to measure the statistical significance of this set. Various procedures exist for controlling the FDR. However the threshold (generally 5%) is arbitrary and a specific measure associated with each gene would be worthwhile. Using process intensity estimation methods, we define and give estimates of the local FDR, which may be considered as the probability for a gene to be a false positive. After a global assessment rule controlling the false positive error, the local FDR is a valuable guideline for deciding wether a gene is differentially expressed. The interest of the method is illustrated on three well known data sets. A R routine for computing local FDR estimates from p-values is available at http://www.i...